Fruit Flies and Circadian Rhythms
Gregory J. Matthews and Sebastian Kirkpatrick
2024-05-28
Fruit Flies
Using the R package suggested by Mads, DiscoRhythm, we performed our analysis on the data provided. We first formatted the data for the package. We named the samples in terms of Circular time, which was two replicates of two 24 hour cycles. We got rid of the “pool - pool” group and did some cleaning so that the replicates all had the same respective treatment names. Those were:
- iso: control
- clk856: brain clock off
- trf: time-restricted feeding
- to: fat-body clock off
We then performed three separate tests for each treatment with the three time phases given: 8, 12, and 24 hours. Those test were the Cosinor (CS), JTK Cycle (JTK), and the Lomb-Scargle (LS), all performed through DiscoRhythm. The results provided the metabolites with significant cycles for that chosen period.
Our results found two main things:
- First, we found metabolites with a 24 hour cycle in the trf group.
- Second, we found significant metabolites at the 12 hour period in the control group.
To display these findings, we presented tables for the the metabolites with the 20 smallest p-values. These q-values presented in these tables are the adjusted p-values using the Benjamini-Hochberg procedure.
In addition to the tables, we used Manhattan plots to visually display the p-values (the red line on each plot is the Bonferroni-adjusted significance level, which is an extremely conservative cut-off).
We then took the metabolites that did have significant cycles, and created graphs of the metabolites versus time to see what those cycles look like.
library(tidyverse)## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
## ✔ dplyr 1.1.4 ✔ readr 2.1.5
## ✔ forcats 1.0.0 ✔ stringr 1.5.1
## ✔ ggplot2 3.5.1 ✔ tibble 3.2.1
## ✔ lubridate 1.9.3 ✔ tidyr 1.3.1
## ✔ purrr 1.0.2
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag() masks stats::lag()
## ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errorslibrary(DiscoRhythm)
test <- as.data.frame(t(read.csv("./MX7590~2(data)_clean_greg.csv", header = FALSE)))
names(test) <- test[1,]
test <- test[-1,]
#table(test$treatment)
#Converting to numeric
test[,9:ncol(test)] <- apply(test[,9:ncol(test)],2,as.numeric)
test <- test %>% filter(treatment != "pool - pool")
test <-
test %>% mutate(
replicate = substr(treatment, nchar(treatment), nchar(treatment)),
trt = substr(treatment, 1, nchar(treatment) - 4),
index = 1:192,
time = rep(seq(0, 46, 2), 8),
c_time = rep(seq(0, 22, 2), 16),
day = rep(rep(c(1, 2), each = 12), 8)
)
test$trt[test$trt == "clock856"] <- "clk856"
names(test) <- gsub(" ", "", names(test))#clk856, iso, to, trf
for (t in c("clk856", "iso", "to", "trf")){
for (p in c(8, 12, 24)){
disco_sub <-
test %>% filter(trt == t) %>% mutate(discoID = paste0("CT", c_time, "_", index, "_", replicate)) %>% select(c(9:584, 590))
t_disco_sub <- as.data.frame(t(disco_sub[, -ncol(disco_sub)]))
names(t_disco_sub) <- test %>% filter(trt == t) %>% mutate(discoID = paste0("CT", c_time, "_", index, "_", replicate)) %>% pull(discoID)
t_disco_sub$IDs <- row.names(t_disco_sub)
t_disco_sub <- t_disco_sub %>% relocate(IDs)
indata <- t_disco_sub
#Converting dfrom DF to SE object.
se <- discoDFtoSE(indata)
#Check input
selectDataSE <- discoCheckInput(se)
results <- discoODAs(selectDataSE,
period=p,
method=c("JTK","CS", "LS"),
ncores=1,
circular_t=TRUE)
plot(-log(sort(results$JTK$pvalue)), ylim = c(0,15), main = paste("Treatment: ",t," - Period: ", p, " - Test: JTK"), ylab = "-log(p-value)")
abline(h = -log(0.05/length(results$JTK$pvalue)), col = "red")
plot(-log(sort(results$CS$pvalue)), ylim = c(0,15), main = paste("Treatment: ",t," - Period: ", p, " - Test: CS"), ylab = "-log(p-value)")
abline(h = -log(0.05/length(results$CS$pvalue)), col = "red")
plot(-log(sort(results$LS$pvalue)), ylim = c(0,15), main = paste("Treatment: ",t," - Period: ", p, " - Test: LS"), ylab = "-log(p-value)")
abline(h = -log(0.05/length(results$LS$pvalue)), col = "red")
print("JTK smallest p-values")
knitr::kable(results$JTK %>% arrange(pvalue) %>% head(20), format = "markdown") %>% print()
print("CS smallest p-values")
knitr::kable(results$CS %>% select(1:4) %>% arrange(pvalue) %>% head(20), format = "markdown") %>% print()
print("LS smallest p-values")
knitr::kable(results$LS %>% arrange(pvalue) %>% head(20), format = "markdown") %>% print()
}
}
## [1] "JTK smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue| period|
## |:-------------------|---------:|----------:|---------:|------:|------:|
## |117986 | 4| 1778.5503| 0.0049075| 1| 8|
## |121476 | 5| 266.5793| 0.0134625| 1| 8|
## |65017 | 4| 2460.3780| 0.0186430| 1| 8|
## |365909 | 6| 412.9504| 0.0227918| 1| 8|
## |histidine | 5| 18115.3686| 0.0241219| 1| 8|
## |514158 | 5| 655.4880| 0.0269912| 1| 8|
## |tryptophan | 5| 4546.6966| 0.0336532| 1| 8|
## |170319 | 0| 300.1668| 0.0336532| 1| 8|
## |106344 | 4| 1067.7312| 0.0355306| 1| 8|
## |351039 | 3| 3522.2757| 0.0374997| 1| 8|
## |N-acetylmannosamine | 6| 269.0541| 0.0428624| 1| 8|
## |377304 | 1| 129.0470| 0.0476146| 1| 8|
## |553346 | 3| 155.5635| 0.0615655| 1| 8|
## |320876 | 5| 218.8495| 0.0751641| 1| 8|
## |379895 | 0| 123.7437| 0.0789443| 1| 8|
## |indole-3-acetate | 5| 336.5828| 0.0828874| 1| 8|
## |mannoheptulose | 5| 277.8930| 0.0890976| 1| 8|
## |uracil | 7| 2793.7789| 0.0980292| 1| 8|
## |241383 | 5| 253.4978| 0.0980292| 1| 8|
## |104131 | 4| 1624.5778| 0.1027755| 1| 8|
## [1] "CS smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue|
## |:-------------------|---------:|----------:|---------:|---------:|
## |117986 | 3.9608044| 2239.0609| 0.0033871| 0.9994387|
## |514158 | 4.0908388| 1119.3476| 0.0099947| 0.9994387|
## |351039 | 2.7700901| 4904.4172| 0.0129921| 0.9994387|
## |106344 | 3.8342893| 1634.1540| 0.0139345| 0.9994387|
## |377304 | 0.5575829| 228.9373| 0.0337072| 0.9994387|
## |121476 | 4.3405507| 414.7903| 0.0372585| 0.9994387|
## |phenol | 0.1317250| 1170.0478| 0.0427905| 0.9994387|
## |pyrophosphate | 7.7766770| 65410.4080| 0.0458140| 0.9994387|
## |65017 | 3.3934821| 3286.9314| 0.0485324| 0.9994387|
## |110328 | 0.6245086| 1210.2232| 0.0505389| 0.9994387|
## |campesterol | 5.6190216| 7144.0149| 0.0508284| 0.9994387|
## |N-acetylmannosamine | 5.1323194| 312.1334| 0.0513269| 0.9994387|
## |241383 | 4.2189763| 508.1212| 0.0516580| 0.9994387|
## |553346 | 2.5785237| 251.1026| 0.0520328| 0.9994387|
## |170319 | 7.4477923| 346.0376| 0.0594115| 0.9994387|
## |104957 | 2.4175900| 963.2616| 0.0650795| 0.9994387|
## |histidine | 4.3885915| 29102.4484| 0.0673772| 0.9994387|
## |146585 | 7.5780991| 722.6006| 0.0703408| 0.9994387|
## |62409 | 0.0289106| 890.0628| 0.0733217| 0.9994387|
## |131450 | 4.2843308| 5662.9493| 0.0849854| 0.9994387|
## [1] "LS smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue| period|
## |:-------------------|---------:|----------:|---------:|------:|------:|
## |117986 | 4.0916443| 6835.039| 0.2435220| 1| 8|
## |514158 | 3.3488549| 7145.252| 0.4976778| 1| 8|
## |351039 | 0.5816402| 20337.892| 0.5782172| 1| 8|
## |106344 | 4.1500588| 8119.103| 0.6004721| 1| 8|
## |377304 | 2.0301353| 2405.441| 0.8671555| 1| 8|
## |121476 | 5.9999190| 3098.066| 0.8906415| 1| 8|
## |phenol | 0.0328433| 10328.999| 0.9191919| 1| 8|
## |pyrophosphate | 7.3977911| 626876.785| 0.9315018| 1| 8|
## |65017 | 6.1104177| 18207.234| 0.9409614| 1| 8|
## |110328 | 0.1319852| 10527.816| 0.9470971| 1| 8|
## |campesterol | 4.2807700| 72550.151| 0.9479284| 1| 8|
## |N-acetylmannosamine | 4.1512747| 2222.239| 0.9493293| 1| 8|
## |241383 | 0.9036704| 4164.298| 0.9502387| 1| 8|
## |553346 | 2.0989285| 1259.943| 0.9512488| 1| 8|
## |170319 | 5.9314155| 2551.613| 0.9674602| 1| 8|
## |104957 | 1.9998024| 6840.423| 0.9761681| 1| 8|
## |histidine | 1.5953091| 146670.273| 0.9790005| 1| 8|
## |146585 | 0.9142193| 6199.121| 0.9821671| 1| 8|
## |62409 | 2.3287742| 14741.902| 0.9848756| 1| 8|
## |131450 | 3.8098581| 74368.455| 0.9920887| 1| 8|
## [1] "JTK smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue| period|
## |:--------------|---------:|---------:|---------:|--------:|------:|
## |lignocericacid | 8| 1132.0780| 0.0032392| 0.852194| 12|
## |14730 | 9| 894.4901| 0.0039982| 0.852194| 12|
## |18256 | 9| 771.4535| 0.0044385| 0.852194| 12|
## |65238 | 10| 1041.2147| 0.0131392| 1.000000| 12|
## |84223 | 6| 3021.8208| 0.0178931| 1.000000| 12|
## |aconiticacid | 9| 1906.0063| 0.0256091| 1.000000| 12|
## |84388 | 4| 1306.0262| 0.0263805| 1.000000| 12|
## |514150 | 4| 731.1484| 0.0304890| 1.000000| 12|
## |cerotinicacid | 9| 224.5064| 0.0382811| 1.000000| 12|
## |553408 | 9| 806.8088| 0.0382811| 1.000000| 12|
## |111253 | 6| 1983.0810| 0.0382811| 1.000000| 12|
## |390130 | 2| 895.5507| 0.0428047| 1.000000| 12|
## |553269 | 10| 1889.7429| 0.0477961| 1.000000| 12|
## |399721 | 2| 288.8531| 0.0504798| 1.000000| 12|
## |110328 | 10| 972.2718| 0.0532958| 1.000000| 12|
## |106686 | 9| 752.8919| 0.0659943| 1.000000| 12|
## |20330 | 6| 1881.6111| 0.0812756| 1.000000| 12|
## |117998 | 3| 4473.1575| 0.0855476| 1.000000| 12|
## |62840 | 3| 9587.4841| 0.0900142| 1.000000| 12|
## |125882 | 8| 1946.6650| 0.0946823| 1.000000| 12|
## [1] "CS smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue|
## |:------------------|---------:|----------:|---------:|---------:|
## |14730 | 8.450995| 905.2258| 0.0006982| 0.4021716|
## |18256 | 8.500485| 784.1888| 0.0018754| 0.5401137|
## |lignocericacid | 7.808949| 1257.7670| 0.0028190| 0.5412495|
## |84223 | 5.243923| 4322.0279| 0.0136198| 0.9989415|
## |390130 | 2.479778| 1146.9375| 0.0215574| 0.9989415|
## |84388 | 4.168673| 1326.3359| 0.0226772| 0.9989415|
## |cerotinicacid | 8.329219| 308.8269| 0.0283023| 0.9989415|
## |65238 | 8.970528| 1151.6261| 0.0294271| 0.9989415|
## |111253 | 5.797932| 3089.5682| 0.0331619| 0.9989415|
## |553376 | 9.148002| 26179.9257| 0.0434108| 0.9989415|
## |514150 | 2.749142| 948.2022| 0.0439192| 0.9989415|
## |4-aminobutyricacid | 8.249401| 11846.0270| 0.0468851| 0.9989415|
## |1,2,4-benzenetriol | 9.550060| 542.3135| 0.0482633| 0.9989415|
## |126350 | 9.342701| 20172.7224| 0.0516183| 0.9989415|
## |342717 | 3.048404| 96118.4432| 0.0519009| 0.9989415|
## |30962 | 5.769866| 2568.1006| 0.0525163| 0.9989415|
## |62840 | 1.910602| 8483.6882| 0.0562506| 0.9989415|
## |87877 | 10.990157| 23854.9504| 0.0604296| 0.9989415|
## |26899 | 9.510716| 505.3903| 0.0612257| 0.9989415|
## |350847 | 11.069068| 2492.6797| 0.0630201| 0.9989415|
## [1] "LS smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue| period|
## |:------------------|----------:|----------:|---------:|------:|------:|
## |14730 | 8.3138173| 5615.438| 0.0776672| 1| 12|
## |18256 | 8.3701511| 5377.063| 0.1594376| 1| 12|
## |lignocericacid | 8.0113774| 7780.238| 0.2137854| 1| 12|
## |84223 | 4.7456171| 32420.855| 0.5931879| 1| 12|
## |390130 | 2.6406326| 8675.745| 0.7401977| 1| 12|
## |84388 | 5.4491858| 6411.941| 0.7559067| 1| 12|
## |cerotinicacid | 10.2142769| 2270.961| 0.8212063| 1| 12|
## |65238 | 10.1053291| 7566.159| 0.8319464| 1| 12|
## |111253 | 4.9064963| 20282.553| 0.8631223| 1| 12|
## |553376 | 9.8073807| 197444.979| 0.9218862| 1| 12|
## |514150 | 2.2432850| 8015.341| 0.9240269| 1| 12|
## |4-aminobutyricacid | 8.0232616| 57931.293| 0.9353977| 1| 12|
## |1,2,4-benzenetriol | 9.2337904| 2645.651| 0.9400863| 1| 12|
## |126350 | 10.1100419| 101537.122| 0.9501306| 1| 12|
## |342717 | 1.8316437| 506737.307| 0.9508957| 1| 12|
## |30962 | 5.4285551| 16125.932| 0.9525219| 1| 12|
## |62840 | 1.9264632| 78981.657| 0.9613023| 1| 12|
## |87877 | 11.1623208| 63104.304| 0.9692285| 1| 12|
## |26899 | 9.8587460| 5270.501| 0.9705445| 1| 12|
## |350847 | 0.1266452| 16232.920| 0.9733100| 1| 12|
## [1] "JTK smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue| period|
## |:---------------------------|---------:|-----------:|---------:|------:|------:|
## |glucose | 14| 213871.1635| 0.0147226| 1| 24|
## |354256 | 15| 517.0718| 0.0147226| 1| 24|
## |480021 | 11| 434.5171| 0.0210632| 1| 24|
## |210229 | 16| 212.8391| 0.0224509| 1| 24|
## |217691 | 15| 6458.1830| 0.0279733| 1| 24|
## |18488 | 13| 1178.5702| 0.0279733| 1| 24|
## |tagatose | 13| 2344.4125| 0.0357862| 1| 24|
## |aminomalonicacid | 17| 3740.9484| 0.0357862| 1| 24|
## |16747 | 15| 7546.5971| 0.0380242| 1| 24|
## |4219 | 15| 2713.5223| 0.0380242| 1| 24|
## |474224 | 3| 65270.5521| 0.0482909| 1| 24|
## |474135 | 3| 60607.5364| 0.0482909| 1| 24|
## |222298 | 15| 1036.6185| 0.0512183| 1| 24|
## |527023 | 18| 678.8225| 0.0543037| 1| 24|
## |citrulline | 14| 7855.6028| 0.0575543| 1| 24|
## |4550 | 18| 9647.5881| 0.0575543| 1| 24|
## |189391 | 15| 261.2760| 0.0627801| 1| 24|
## |187855 | 15| 729.7342| 0.0627801| 1| 24|
## |3-Aminopiperidine-2,6-dione | 19| 3613.4924| 0.0645822| 1| 24|
## |1-docosanol | 16| 429.9209| 0.0645822| 1| 24|
## [1] "CS smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue|
## |:----------------|---------:|----------:|---------:|---------:|
## |222298 | 14.410007| 1432.9249| 0.0057593| 0.6674312|
## |4219 | 14.194488| 3077.3675| 0.0069491| 0.6674312|
## |379063 | 17.219622| 1780.4416| 0.0076828| 0.6674312|
## |210229 | 14.850058| 295.9127| 0.0079556| 0.6674312|
## |18488 | 12.950271| 1173.6382| 0.0090144| 0.6674312|
## |16747 | 14.045778| 11041.9861| 0.0093705| 0.6674312|
## |17537 | 11.062843| 878.3176| 0.0103553| 0.6674312|
## |4550 | 17.007741| 9148.1711| 0.0121899| 0.6674312|
## |1-docosanol | 16.240900| 476.2339| 0.0164550| 0.6674312|
## |189391 | 14.731576| 359.6343| 0.0170700| 0.6674312|
## |104933 | 13.394109| 3546.2902| 0.0173377| 0.6674312|
## |1771 | 16.796222| 544.0125| 0.0175568| 0.6674312|
## |320876 | 18.433396| 353.1520| 0.0176739| 0.6674312|
## |aminomalonicacid | 16.161535| 4208.6371| 0.0180061| 0.6674312|
## |527091 | 19.266612| 847.6074| 0.0184198| 0.6674312|
## |474224 | 1.762252| 77143.0933| 0.0185398| 0.6674312|
## |412156 | 9.933017| 315.5222| 0.0218689| 0.7409682|
## |474135 | 1.931885| 68581.6832| 0.0269694| 0.7762484|
## |125897 | 13.947191| 14661.5724| 0.0283548| 0.7762484|
## |1867 | 4.926583| 1337.2059| 0.0305439| 0.7762484|
## [1] "LS smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue| period|
## |:----------------|---------:|----------:|---------:|------:|------:|
## |222298 | 13.595129| 7687.959| 0.3508564| 1| 24|
## |4219 | 13.812488| 11689.763| 0.3969245| 1| 24|
## |379063 | 17.117229| 8439.777| 0.4232774| 1| 24|
## |210229 | 14.091732| 2296.530| 0.4327124| 1| 24|
## |18488 | 12.138354| 8076.626| 0.4676109| 1| 24|
## |16747 | 14.129621| 73051.817| 0.4787696| 1| 24|
## |17537 | 10.188079| 6379.174| 0.5082365| 1| 24|
## |4550 | 16.603029| 82644.988| 0.5581884| 1| 24|
## |1-docosanol | 12.146050| 2894.729| 0.6539461| 1| 24|
## |189391 | 12.383998| 2988.710| 0.6657864| 1| 24|
## |104933 | 12.540415| 21325.258| 0.6708052| 1| 24|
## |1771 | 17.258443| 4045.552| 0.6748532| 1| 24|
## |320876 | 18.957032| 4200.523| 0.6769934| 1| 24|
## |aminomalonicacid | 17.963673| 18506.452| 0.6829873| 1| 24|
## |527091 | 17.818706| 4355.431| 0.6902866| 1| 24|
## |474224 | 3.202457| 455724.440| 0.6923706| 1| 24|
## |412156 | 13.508391| 2366.413| 0.7446703| 1| 24|
## |474135 | 3.016576| 462162.276| 0.8075664| 1| 24|
## |125897 | 15.788896| 68813.965| 0.8217232| 1| 24|
## |1867 | 4.815662| 11414.723| 0.8419596| 1| 24|
## [1] "JTK smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue| period|
## |:-----------------|---------:|----------:|---------:|------:|------:|
## |370221 | 4| 4046.4186| 0.0063728| 1| 8|
## |124996 | 1| 1709.4306| 0.0285364| 1| 8|
## |20281 | 6| 9652.1843| 0.0463712| 1| 8|
## |1-monopalmitin | 7| 476.2364| 0.0514606| 1| 8|
## |65017 | 5| 1322.2897| 0.0514606| 1| 8|
## |437830 | 5| 662.5591| 0.0570318| 1| 8|
## |381422 | 0| 11466.4436| 0.0570318| 1| 8|
## |87877 | 6| 9829.1378| 0.0570318| 1| 8|
## |33282 | 5| 4772.0869| 0.0570318| 1| 8|
## |390130 | 0| 592.2019| 0.0733141| 1| 8|
## |189391 | 1| 184.9084| 0.0733141| 1| 8|
## |110328 | 1| 776.7568| 0.0733141| 1| 8|
## |351245 | 5| 103.0608| 0.0849004| 1| 8|
## |110321 | 0| 283.5498| 0.0849004| 1| 8|
## |octadecylglycerol | 4| 4363.3792| 0.0890976| 1| 8|
## |514150 | 5| 683.7723| 0.0890976| 1| 8|
## |33142 | 5| 2576.8739| 0.0890976| 1| 8|
## |tagatose | 5| 1852.0894| 0.0934720| 1| 8|
## |behenicacid | 1| 10527.4058| 0.0980292| 1| 8|
## |377239 | 4| 375.8273| 0.0980292| 1| 8|
## [1] "CS smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue|
## |:------------------------|---------:|----------:|---------:|--------:|
## |370221 | 3.9051854| 5172.0421| 0.0067636| 0.998439|
## |124996 | 7.3738910| 4181.9797| 0.0081907| 0.998439|
## |arachidicacid | 7.4984513| 4955.6173| 0.0151275| 0.998439|
## |1-monopalmitin | 7.0593182| 552.2899| 0.0168864| 0.998439|
## |381422 | 7.1660103| 11117.5118| 0.0344256| 0.998439|
## |stearicacid | 0.4797160| 56125.5160| 0.0402616| 0.998439|
## |7490 | 4.3189010| 8350.8596| 0.0429932| 0.998439|
## |146585 | 0.5840764| 443.5667| 0.0437199| 0.998439|
## |octadecylglycerol | 3.4987406| 5629.1701| 0.0558883| 0.998439|
## |376823 | 3.9093869| 1123.3018| 0.0560193| 0.998439|
## |241383 | 6.1700670| 478.3861| 0.0584504| 0.998439|
## |62409 | 0.3126371| 624.9538| 0.0586469| 0.998439|
## |437830 | 4.4856342| 680.3493| 0.0597446| 0.998439|
## |sedoheptulose7-phosphate | 1.3439412| 3123.1768| 0.0749164| 0.998439|
## |cysteine | 4.0517487| 2430.3404| 0.0754800| 0.998439|
## |592429 | 6.4055609| 641.6954| 0.0812641| 0.998439|
## |84223 | 6.3417223| 2294.2173| 0.0821751| 0.998439|
## |117742 | 3.8915828| 39183.3414| 0.0826896| 0.998439|
## |104663 | 7.9528858| 184.7098| 0.0829994| 0.998439|
## |223087 | 4.9774080| 5300.4819| 0.0842956| 0.998439|
## [1] "LS smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue| period|
## |:------------------------|---------:|----------:|---------:|------:|------:|
## |370221 | 3.836196| 17052.433| 0.3900235| 1| 8|
## |124996 | 4.972816| 34052.822| 0.4406953| 1| 8|
## |arachidicacid | 6.067523| 26476.904| 0.6268224| 1| 8|
## |1-monopalmitin | 7.977545| 3023.194| 0.6622980| 1| 8|
## |381422 | 7.791549| 144606.156| 0.8722862| 1| 8|
## |stearicacid | 2.526317| 702474.810| 0.9072095| 1| 8|
## |7490 | 3.996268| 49491.449| 0.9200826| 1| 8|
## |146585 | 4.733638| 5374.678| 0.9231950| 1| 8|
## |octadecylglycerol | 5.549911| 42339.363| 0.9605265| 1| 8|
## |376823 | 4.255625| 13469.646| 0.9608087| 1| 8|
## |241383 | 6.441958| 4132.071| 0.9656985| 1| 8|
## |62409 | 0.000081| 14284.029| 0.9660664| 1| 8|
## |437830 | 4.019449| 10079.288| 0.9680497| 1| 8|
## |sedoheptulose7-phosphate | 2.004631| 16245.052| 0.9861533| 1| 8|
## |cysteine | 5.999921| 13611.417| 0.9865789| 1| 8|
## |592429 | 7.966204| 3850.129| 0.9902655| 1| 8|
## |84223 | 5.293376| 33372.930| 0.9907468| 1| 8|
## |117742 | 2.350027| 636833.342| 0.9910082| 1| 8|
## |104663 | 6.084911| 3769.620| 0.9911621| 1| 8|
## |223087 | 5.999919| 27989.679| 0.9917782| 1| 8|
## [1] "JTK smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue| period|
## |:------------|---------:|----------:|---------:|---------:|------:|
## |342000 | 6| 1537.9572| 0.0001625| 0.0510576| 12|
## |479 | 6| 3672.7126| 0.0001773| 0.0510576| 12|
## |levoglucosan | 1| 4339.1608| 0.0006694| 0.1285277| 12|
## |520873 | 1| 1731.7045| 0.0019543| 0.2606293| 12|
## |344945 | 4| 1951.9683| 0.0022624| 0.2606293| 12|
## |65017 | 1| 1799.5868| 0.0037287| 0.2878709| 12|
## |120562 | 6| 2916.6387| 0.0039982| 0.2878709| 12|
## |18256 | 6| 830.4969| 0.0039982| 0.2878709| 12|
## |210297 | 6| 10310.6775| 0.0052647| 0.3369400| 12|
## |124996 | 6| 3812.3662| 0.0068893| 0.3968211| 12|
## |406851 | 2| 806.1017| 0.0083949| 0.4395898| 12|
## |4550 | 5| 5853.4299| 0.0108685| 0.5216871| 12|
## |408463 | 5| 18336.6930| 0.0148832| 0.6079248| 12|
## |354256 | 11| 767.2109| 0.0148832| 0.6079248| 12|
## |67160 | 4| 3301.4816| 0.0158314| 0.6079248| 12|
## |356988 | 0| 193.0402| 0.0196029| 0.6861152| 12|
## |371565 | 5| 322.2639| 0.0214411| 0.6861152| 12|
## |323785 | 1| 3006.9716| 0.0214411| 0.6861152| 12|
## |125882 | 6| 3904.9972| 0.0256091| 0.7763611| 12|
## |599196 | 10| 2869.4393| 0.0304890| 0.8166641| 12|
## [1] "CS smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue|
## |:------------|----------:|----------:|---------:|---------:|
## |levoglucosan | 11.8699892| 4694.8321| 0.0000693| 0.0347211|
## |520873 | 0.2889131| 2407.4098| 0.0001591| 0.0347211|
## |342000 | 5.7164341| 1811.6613| 0.0001808| 0.0347211|
## |479 | 5.1841295| 5058.9617| 0.0012251| 0.1527624|
## |67160 | 3.9890233| 4350.9677| 0.0014589| 0.1527624|
## |323785 | 0.0748233| 3815.9698| 0.0017362| 0.1527624|
## |18256 | 6.2729662| 950.2516| 0.0018565| 0.1527624|
## |210297 | 5.0591104| 13937.9567| 0.0031662| 0.2279692|
## |354256 | 10.7439736| 1002.4332| 0.0038134| 0.2440548|
## |408463 | 5.1051958| 23828.7419| 0.0043980| 0.2475575|
## |4550 | 4.7814818| 8125.5672| 0.0049785| 0.2475575|
## |344945 | 4.2467268| 2619.4946| 0.0053993| 0.2475575|
## |406851 | 0.6637997| 1073.3918| 0.0058884| 0.2475575|
## |120562 | 5.4543857| 3003.3961| 0.0060170| 0.2475575|
## |124996 | 5.2247746| 4201.6119| 0.0077877| 0.2990460|
## |17174 | 4.5219686| 322.0574| 0.0093348| 0.3360530|
## |371565 | 4.6520692| 406.6160| 0.0114549| 0.3881181|
## |599196 | 9.0630890| 5124.5421| 0.0124900| 0.3996789|
## |26736 | 3.5547729| 433.4540| 0.0142873| 0.4331297|
## |shikimicacid | 0.6910786| 10084.1749| 0.0156094| 0.4495499|
## [1] "LS smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue| period|
## |:------------|----------:|----------:|---------:|------:|------:|
## |levoglucosan | 11.9033700| 15216.248| 0.0152378| 1| 12|
## |520873 | 0.1568281| 9366.124| 0.0270008| 1| 12|
## |342000 | 6.0058638| 11862.473| 0.0295384| 1| 12|
## |479 | 5.5309696| 45922.650| 0.1169757| 1| 12|
## |67160 | 3.8996415| 28185.022| 0.1328460| 1| 12|
## |323785 | 0.1071321| 22223.244| 0.1507641| 1| 12|
## |18256 | 5.0182714| 5940.656| 0.1582710| 1| 12|
## |210297 | 5.4969316| 78801.124| 0.2321884| 1| 12|
## |354256 | 10.1802636| 5659.961| 0.2646486| 1| 12|
## |408463 | 5.0274038| 158332.209| 0.2921860| 1| 12|
## |4550 | 5.9301666| 80981.837| 0.3180716| 1| 12|
## |344945 | 3.9858758| 20746.174| 0.3360124| 1| 12|
## |406851 | 0.4693507| 6354.641| 0.3560696| 1| 12|
## |120562 | 6.0492436| 46986.356| 0.3612112| 1| 12|
## |124996 | 4.9728157| 34052.822| 0.4269268| 1| 12|
## |17174 | 6.1775070| 3061.450| 0.4776648| 1| 12|
## |371565 | 4.6581113| 3328.086| 0.5388989| 1| 12|
## |599196 | 8.5009032| 33638.456| 0.5658010| 1| 12|
## |26736 | 2.9261505| 2774.836| 0.6084689| 1| 12|
## |shikimicacid | 0.3409416| 32940.743| 0.6369236| 1| 12|
## [1] "JTK smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue| period|
## |:-------------|---------:|----------:|---------:|--------:|------:|
## |43734 | 14| 1716.3249| 0.0016962| 0.976985| 24|
## |366008 | 14| 4140.4638| 0.0060345| 1.000000| 24|
## |117260 | 5| 1710.6681| 0.0060345| 1.000000| 24|
## |14730 | 22| 674.7566| 0.0098352| 1.000000| 24|
## |tagatose | 2| 3924.0891| 0.0246771| 1.000000| 24|
## |527023 | 23| 393.1514| 0.0307146| 1.000000| 24|
## |109995 | 13| 3879.3646| 0.0403876| 1.000000| 24|
## |phenylalanine | 12| 4123.8467| 0.0428822| 1.000000| 24|
## |167348 | 12| 26170.9059| 0.0455145| 1.000000| 24|
## |342717 | 11| 64347.4242| 0.0512183| 1.000000| 24|
## |aconiticacid | 1| 2316.1283| 0.0609779| 1.000000| 24|
## |31764 | 4| 374.2363| 0.0609779| 1.000000| 24|
## |599103 | 14| 1676.5502| 0.0683754| 1.000000| 24|
## |371544 | 13| 183.4942| 0.0703706| 1.000000| 24|
## |371546 | 15| 5088.3404| 0.0765623| 1.000000| 24|
## |210279 | 16| 5683.7243| 0.0856093| 1.000000| 24|
## |42424 | 13| 888.8332| 0.0955922| 1.000000| 24|
## |18256 | 22| 593.0858| 0.0955922| 1.000000| 24|
## |553492 | 21| 1392.6468| 0.1251859| 1.000000| 24|
## |117199 | 13| 968.3827| 0.1355512| 1.000000| 24|
## [1] "CS smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue|
## |:---------------|----------:|----------:|---------:|---------:|
## |117260 | 3.3158463| 1932.3448| 0.0016905| 0.9382886|
## |14730 | 21.6099181| 952.3756| 0.0089360| 0.9382886|
## |210279 | 16.1174214| 6440.8457| 0.0108190| 0.9382886|
## |43734 | 12.4246169| 4024.3865| 0.0178321| 0.9382886|
## |534527 | 0.1431518| 3110.1694| 0.0193303| 0.9382886|
## |366008 | 13.4501149| 8322.8602| 0.0227516| 0.9382886|
## |167348 | 11.9272357| 25860.4693| 0.0242307| 0.9382886|
## |aconiticacid | 23.4642136| 2838.7311| 0.0280865| 0.9382886|
## |599103 | 14.4021750| 2605.8821| 0.0294202| 0.9382886|
## |125897 | 18.6349454| 14302.9456| 0.0308738| 0.9382886|
## |109995 | 12.9572189| 4670.8087| 0.0316128| 0.9382886|
## |527023 | 22.4883886| 601.1685| 0.0322592| 0.9382886|
## |42424 | 12.8013080| 896.1066| 0.0332183| 0.9382886|
## |pantothenicacid | 17.9197980| 932.6786| 0.0333281| 0.9382886|
## |18488 | 22.7904955| 1139.8055| 0.0337924| 0.9382886|
## |342717 | 10.5162057| 84193.8364| 0.0363617| 0.9382886|
## |butane-2,3-diol | 14.3667083| 14235.3941| 0.0375959| 0.9382886|
## |133612 | 14.3977927| 2939.9010| 0.0384373| 0.9382886|
## |351222 | 19.0491750| 433.2302| 0.0393235| 0.9382886|
## |371271 | 10.9620388| 6437.3416| 0.0399113| 0.9382886|
## [1] "LS smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue| period|
## |:---------------|---------:|----------:|---------:|------:|------:|
## |117260 | 4.752231| 11902.651| 0.1478743| 1| 24|
## |14730 | 4.158996| 5955.829| 0.4651185| 1| 24|
## |210279 | 14.656897| 42281.479| 0.5214415| 1| 24|
## |43734 | 12.118934| 13510.162| 0.6798630| 1| 24|
## |534527 | 21.999959| 24511.592| 0.7057330| 1| 24|
## |366008 | 12.193984| 40916.270| 0.7569145| 1| 24|
## |167348 | 10.600262| 390683.465| 0.7760834| 1| 24|
## |aconiticacid | 4.027791| 14498.919| 0.8190669| 1| 24|
## |599103 | 12.407606| 20349.607| 0.8318830| 1| 24|
## |125897 | 21.999947| 67547.789| 0.8448001| 1| 24|
## |109995 | 12.079811| 41261.316| 0.8509748| 1| 24|
## |527023 | 0.000081| 3942.499| 0.8561712| 1| 24|
## |42424 | 12.442864| 11729.814| 0.8635451| 1| 24|
## |pantothenicacid | 16.962025| 11768.946| 0.8643650| 1| 24|
## |18488 | 19.768860| 7227.517| 0.8677751| 1| 24|
## |342717 | 13.808775| 595702.748| 0.8851384| 1| 24|
## |butane-2,3-diol | 14.238654| 143369.445| 0.8926424| 1| 24|
## |133612 | 12.545836| 22364.073| 0.8974732| 1| 24|
## |351222 | 14.142649| 5020.000| 0.9023248| 1| 24|
## |371271 | 13.798721| 39220.912| 0.9054148| 1| 24|
## [1] "JTK smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue| period|
## |:------------------|---------:|------------:|---------:|------:|------:|
## |43734 | 7| 1765.64563| 0.0072457| 1| 8|
## |414391 | 7| 86.62058| 0.0221596| 1| 8|
## |378996 | 3| 5040.96424| 0.0241219| 1| 8|
## |17537 | 7| 514.06663| 0.0336532| 1| 8|
## |4986 | 3| 2227.03281| 0.0374997| 1| 8|
## |474135 | 3| 108358.28059| 0.0488579| 1| 8|
## |130717 | 1| 850.29590| 0.0488579| 1| 8|
## |18156 | 6| 8271.02802| 0.0541837| 1| 8|
## |3-phosphoglycerate | 3| 863.37738| 0.0647473| 1| 8|
## |412156 | 4| 178.36769| 0.0849004| 1| 8|
## |224193 | 2| 801.32876| 0.0890976| 1| 8|
## |67160 | 2| 2743.92786| 0.0890976| 1| 8|
## |377510 | 2| 429.92092| 0.0934720| 1| 8|
## |glucose | 0| 154972.35059| 0.0980292| 1| 8|
## |88910 | 0| 240.94664| 0.0980292| 1| 8|
## |42525 | 1| 982.17132| 0.0980292| 1| 8|
## |1867 | 2| 980.75711| 0.1027755| 1| 8|
## |371541 | 4| 181.72644| 0.1128593| 1| 8|
## |panose | 5| 2923.53299| 0.1182094| 1| 8|
## |163829 | 6| 6246.58130| 0.1182094| 1| 8|
## [1] "CS smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue|
## |:-----------|---------:|-----------:|---------:|---------:|
## |414391 | 5.9767902| 123.4372| 0.0029145| 0.9940224|
## |378996 | 2.7536783| 5368.5687| 0.0128314| 0.9940224|
## |18156 | 5.4758140| 8637.4167| 0.0150678| 0.9940224|
## |maltotriose | 4.7494327| 8256.2632| 0.0227291| 0.9940224|
## |357049 | 5.4301311| 417.3601| 0.0253755| 0.9940224|
## |43734 | 6.6763914| 1599.1417| 0.0387727| 0.9940224|
## |474135 | 2.2423898| 115833.6303| 0.0406550| 0.9940224|
## |14730 | 4.7064387| 539.8122| 0.0434311| 0.9940224|
## |130717 | 0.5647406| 1028.1095| 0.0456900| 0.9940224|
## |412156 | 3.5286644| 189.6824| 0.0506737| 0.9940224|
## |399721 | 0.3537437| 1595.3000| 0.0555726| 0.9940224|
## |553492 | 7.3368022| 2308.5689| 0.0571540| 0.9940224|
## |224193 | 1.2891386| 883.1947| 0.0592437| 0.9940224|
## |417938 | 5.8673621| 1159.6198| 0.0611792| 0.9940224|
## |321064 | 1.5088184| 1915.7061| 0.0632079| 0.9940224|
## |panose | 4.6848376| 3604.6833| 0.0660400| 0.9940224|
## |maltose | 4.8933677| 197883.0402| 0.0666995| 0.9940224|
## |67160 | 1.8646168| 4173.3615| 0.0708479| 0.9940224|
## |17537 | 6.4713920| 525.5688| 0.0759341| 0.9940224|
## |1867 | 2.0357256| 1569.8263| 0.0776546| 0.9940224|
## [1] "LS smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue| period|
## |:-----------|---------:|------------:|---------:|------:|------:|
## |414391 | 5.9425665| 993.1262| 0.2189239| 1| 8|
## |378996 | 4.1321814| 29471.7708| 0.5742854| 1| 8|
## |18156 | 5.9999190| 30496.2726| 0.6255495| 1| 8|
## |maltotriose | 3.9280225| 61393.9005| 0.7566112| 1| 8|
## |357049 | 5.7620125| 3135.0140| 0.7898433| 1| 8|
## |43734 | 0.3413329| 7404.6612| 0.8993369| 1| 8|
## |474135 | 7.8908053| 692739.8941| 0.9091848| 1| 8|
## |14730 | 5.6060401| 5046.5905| 0.9219729| 1| 8|
## |130717 | 0.0000810| 7920.0060| 0.9310361| 1| 8|
## |412156 | 3.5975493| 1645.1476| 0.9474858| 1| 8|
## |399721 | 0.0550369| 6594.7680| 0.9598378| 1| 8|
## |553492 | 7.9691891| 19310.7994| 0.9631716| 1| 8|
## |224193 | 6.9652892| 10602.2931| 0.9671593| 1| 8|
## |417938 | 3.8655381| 8081.5891| 0.9704694| 1| 8|
## |321064 | 1.2834946| 17690.2070| 0.9735841| 1| 8|
## |panose | 3.9585282| 26298.3980| 0.9773953| 1| 8|
## |maltose | 3.9329157| 1406448.9494| 0.9782016| 1| 8|
## |67160 | 2.7735971| 33560.2517| 0.9826596| 1| 8|
## |17537 | 3.9823922| 4665.5242| 0.9869124| 1| 8|
## |1867 | 7.8875403| 13926.9362| 0.9881034| 1| 8|
## [1] "JTK smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue| period|
## |:------------|---------:|----------:|---------:|---------:|------:|
## |17267 | 0| 1177.6863| 0.0019543| 0.9328825| 12|
## |84925 | 5| 1751.1499| 0.0032392| 0.9328825| 12|
## |84388 | 1| 628.9715| 0.0073613| 1.0000000| 12|
## |376823 | 11| 1216.2237| 0.0115824| 1.0000000| 12|
## |4550 | 0| 8497.3022| 0.0214411| 1.0000000| 12|
## |65238 | 1| 1305.3191| 0.0271518| 1.0000000| 12|
## |345436 | 11| 1076.5701| 0.0322911| 1.0000000| 12|
## |553471 | 2| 1217.2843| 0.0341877| 1.0000000| 12|
## |371565 | 1| 281.2517| 0.0341877| 1.0000000| 12|
## |408463 | 1| 28466.3512| 0.0452394| 1.0000000| 12|
## |350847 | 8| 1582.5050| 0.0504798| 1.0000000| 12|
## |aconiticacid | 6| 1044.3967| 0.0532958| 1.0000000| 12|
## |maltotriose | 1| 5306.8364| 0.0659943| 1.0000000| 12|
## |379063 | 1| 902.9754| 0.0659943| 1.0000000| 12|
## |106387 | 5| 1169.2011| 0.0771909| 1.0000000| 12|
## |26736 | 11| 364.5135| 0.0971209| 1.0000000| 12|
## |myo-inositol | 5| 11829.7197| 0.1046532| 1.0000000| 12|
## |levoglucosan | 10| 1050.7607| 0.1046532| 1.0000000| 12|
## |3208 | 5| 2599.5013| 0.1046532| 1.0000000| 12|
## |356984 | 11| 465.6298| 0.1099711| 1.0000000| 12|
## [1] "CS smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue|
## |:-----------------------|----------:|----------:|---------:|---------:|
## |17267 | 11.4722332| 1411.0548| 0.0039041| 0.9977994|
## |553471 | 1.0874765| 1855.5290| 0.0060531| 0.9977994|
## |84388 | 0.7860730| 1052.6835| 0.0069583| 0.9977994|
## |84925 | 4.4003871| 1756.7976| 0.0078605| 0.9977994|
## |350847 | 7.2942078| 1811.1245| 0.0129270| 0.9977994|
## |4550 | 11.5959793| 8147.9701| 0.0155707| 0.9977994|
## |376823 | 10.6341620| 1768.4739| 0.0158644| 0.9977994|
## |408463 | 0.7066031| 26036.7106| 0.0246791| 0.9977994|
## |379063 | 0.3717935| 963.2783| 0.0269801| 0.9977994|
## |135260 | 11.4344147| 285.3809| 0.0356304| 0.9977994|
## |344945 | 11.7260831| 2500.1071| 0.0380043| 0.9977994|
## |aconiticacid | 4.4452849| 1889.3059| 0.0399161| 0.9977994|
## |65238 | 0.7257554| 1296.2858| 0.0405108| 0.9977994|
## |UDP-N-acetylglucosamine | 1.6043694| 905.1217| 0.0410323| 0.9977994|
## |21683 | 11.2022094| 3653.3621| 0.0462387| 0.9977994|
## |345436 | 10.0417605| 988.5905| 0.0472953| 0.9977994|
## |356984 | 10.6923174| 499.1233| 0.0509031| 0.9977994|
## |106387 | 3.9533964| 1788.0115| 0.0592367| 0.9977994|
## |170319 | 7.3364949| 264.2228| 0.0643052| 0.9977994|
## |mevalonicacid | 5.0496670| 2971.6523| 0.0658019| 0.9977994|
## [1] "LS smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue| period|
## |:-----------------------|----------:|----------:|---------:|------:|------:|
## |17267 | 0.0010872| 7503.897| 0.2690287| 1| 12|
## |553471 | 1.2432218| 14826.242| 0.3626454| 1| 12|
## |84388 | 0.1246645| 6177.392| 0.3972634| 1| 12|
## |84925 | 2.5315001| 16706.845| 0.4294437| 1| 12|
## |350847 | 7.7298574| 13761.725| 0.5766293| 1| 12|
## |4550 | 0.2525746| 76124.801| 0.6361244| 1| 12|
## |376823 | 10.0555142| 15026.461| 0.6421503| 1| 12|
## |408463 | 2.1070979| 161868.495| 0.7815804| 1| 12|
## |379063 | 0.4128332| 7206.079| 0.8076796| 1| 12|
## |135260 | 0.0831015| 2801.489| 0.8804446| 1| 12|
## |344945 | 11.9965827| 19837.231| 0.8950148| 1| 12|
## |aconiticacid | 2.2720770| 12189.792| 0.9054400| 1| 12|
## |65238 | 11.8559555| 5520.296| 0.9084659| 1| 12|
## |UDP-N-acetylglucosamine | 1.9515692| 7235.823| 0.9110390| 1| 12|
## |21683 | 10.0995647| 48531.537| 0.9330739| 1| 12|
## |345436 | 9.9182473| 15597.642| 0.9368301| 1| 12|
## |356984 | 10.0154513| 4016.482| 0.9481407| 1| 12|
## |106387 | 2.1118735| 8516.968| 0.9671467| 1| 12|
## |170319 | 7.9780365| 2431.088| 0.9751308| 1| 12|
## |mevalonicacid | 4.4689402| 20493.006| 0.9770971| 1| 12|
## [1] "JTK smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue| period|
## |:------------------------|---------:|-----------:|---------:|------:|------:|
## |gluconicacid | 16| 7124.63115| 0.0052296| 1| 24|
## |42424 | 14| 1017.52666| 0.0167899| 1| 24|
## |104179 | 13| 512.47564| 0.0191184| 1| 24|
## |1-monostearin | 14| 577.35269| 0.0210632| 1| 24|
## |371543 | 13| 242.18407| 0.0288698| 1| 24|
## |2813 | 6| 11252.54376| 0.0336676| 1| 24|
## |2-monoolein | 16| 7277.71977| 0.0380242| 1| 24|
## |377510 | 17| 484.01459| 0.0512183| 1| 24|
## |inosine | 11| 22312.40093| 0.0543037| 1| 24|
## |396734 | 5| 98.46462| 0.0609779| 1| 24|
## |371544 | 13| 202.58609| 0.0645822| 1| 24|
## |1-monopalmitin | 5| 300.34361| 0.0787680| 1| 24|
## |31224 | 18| 2944.74619| 0.0809737| 1| 24|
## |sedoheptulose7-phosphate | 4| 1422.52207| 0.0856093| 1| 24|
## |106344 | 4| 895.90429| 0.0904789| 1| 24|
## |377239 | 16| 985.88363| 0.0955922| 1| 24|
## |87877 | 19| 7925.42958| 0.1251859| 1| 24|
## |threitol | 4| 306.88434| 0.1285873| 1| 24|
## |95422 | 6| 6029.85308| 0.1319886| 1| 24|
## |321064 | 18| 1069.14545| 0.1543818| 1| 24|
## [1] "CS smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue|
## |:------------|---------:|-----------:|---------:|---------:|
## |gluconicacid | 16.101853| 7979.2000| 0.0014067| 0.8102314|
## |104179 | 13.547928| 815.8729| 0.0094430| 0.9926532|
## |monomyristin | 4.002393| 2518.9207| 0.0109466| 0.9926532|
## |2-monoolein | 16.436697| 9056.2894| 0.0142306| 0.9926532|
## |2813 | 5.078088| 14597.2954| 0.0142966| 0.9926532|
## |371544 | 12.346177| 219.5221| 0.0146809| 0.9926532|
## |377510 | 15.627716| 778.6221| 0.0159627| 0.9926532|
## |threitol | 1.838166| 644.0721| 0.0162288| 0.9926532|
## |321064 | 17.152153| 2300.9309| 0.0165599| 0.9926532|
## |377239 | 15.700094| 845.7528| 0.0206774| 0.9926532|
## |95422 | 6.182168| 6516.4834| 0.0267736| 0.9926532|
## |106344 | 4.222153| 2196.7289| 0.0274029| 0.9926532|
## |371543 | 13.674228| 261.2843| 0.0303836| 0.9926532|
## |100934 | 7.325535| 23367.0318| 0.0320148| 0.9926532|
## |31224 | 16.282295| 4866.0530| 0.0322282| 0.9926532|
## |370223 | 13.280774| 5602.4097| 0.0375990| 0.9926532|
## |474135 | 15.816721| 115296.8099| 0.0419688| 0.9926532|
## |371541 | 14.362243| 287.8903| 0.0426271| 0.9926532|
## |380694 | 3.939889| 7761.5392| 0.0428202| 0.9926532|
## |1867 | 16.367643| 1716.1183| 0.0455169| 0.9926532|
## [1] "LS smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue| period|
## |:------------|----------:|----------:|---------:|------:|------:|
## |gluconicacid | 18.0582556| 52416.204| 0.1293658| 1| 24|
## |104179 | 12.0973098| 5941.107| 0.4810089| 1| 24|
## |monomyristin | 4.3092512| 10946.642| 0.5250035| 1| 24|
## |2-monoolein | 16.4724804| 50108.728| 0.6071973| 1| 24|
## |2813 | 3.1658613| 68065.603| 0.6086775| 1| 24|
## |371544 | 12.0546412| 2017.428| 0.6171856| 1| 24|
## |377510 | 15.4800056| 6494.377| 0.6441437| 1| 24|
## |threitol | 0.0000418| 5421.126| 0.6494774| 1| 24|
## |321064 | 17.2834946| 17690.207| 0.6559967| 1| 24|
## |377239 | 15.7559716| 6153.795| 0.7271154| 1| 24|
## |95422 | 5.9685883| 39703.295| 0.8054749| 1| 24|
## |106344 | 4.2334304| 9028.241| 0.8121155| 1| 24|
## |371543 | 12.5020046| 1684.958| 0.8405606| 1| 24|
## |100934 | 6.0517059| 196920.227| 0.8542287| 1| 24|
## |31224 | 12.1498431| 31747.972| 0.8559268| 1| 24|
## |370223 | 12.1826094| 140848.109| 0.8926606| 1| 24|
## |474135 | 15.8908053| 692739.894| 0.9154795| 1| 24|
## |371541 | 13.3354616| 2090.286| 0.9184671| 1| 24|
## |380694 | 2.8701776| 22726.392| 0.9193231| 1| 24|
## |1867 | 15.8875403| 13926.936| 0.9303806| 1| 24|
## [1] "JTK smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue| period|
## |:----------------------|---------:|----------:|---------:|------:|------:|
## |342949 | 7| 813.7031| 0.0059732| 1| 8|
## |65238 | 3| 1253.3468| 0.0067965| 1| 8|
## |390130 | 4| 822.5420| 0.0087595| 1| 8|
## |17537 | 3| 408.7077| 0.0105542| 1| 8|
## |384970 | 5| 320.6729| 0.0126747| 1| 8|
## |zymostenol | 5| 308.6521| 0.0142941| 1| 8|
## |217691 | 3| 16318.6103| 0.0170728| 1| 8|
## |357049 | 4| 693.8485| 0.0203260| 1| 8|
## |3-hydroxypropionicacid | 3| 13615.3411| 0.0301596| 1| 8|
## |474021 | 4| 280.7214| 0.0310119| 1| 8|
## |187871 | 4| 417.9001| 0.0417286| 1| 8|
## |18488 | 3| 835.2699| 0.0417286| 1| 8|
## |210229 | 0| 777.4639| 0.0463712| 1| 8|
## |404049 | 5| 208.5965| 0.0514606| 1| 8|
## |33142 | 4| 11581.3484| 0.0541837| 1| 8|
## |indole-3-acetate | 4| 494.2676| 0.0663730| 1| 8|
## |327608 | 4| 163.3417| 0.0715414| 1| 8|
## |125897 | 4| 12298.7082| 0.0770142| 1| 8|
## |62409 | 4| 669.4533| 0.0770142| 1| 8|
## |20330 | 4| 1088.2373| 0.0770142| 1| 8|
## [1] "CS smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue|
## |:----------------------|---------:|-----------:|---------:|---------:|
## |65238 | 2.1229636| 1684.8092| 0.0015241| 0.8778818|
## |210229 | 7.1350553| 823.1615| 0.0128644| 0.9993075|
## |384970 | 3.8101911| 554.9046| 0.0130077| 0.9993075|
## |indole-3-acetate | 3.4075714| 441.8476| 0.0135950| 0.9993075|
## |217691 | 2.4311656| 26182.5298| 0.0139212| 0.9993075|
## |342949 | 6.2700075| 935.9669| 0.0145556| 0.9993075|
## |glucose | 1.3173563| 176825.0157| 0.0179470| 0.9993075|
## |3-hydroxypropionicacid | 2.3944136| 22860.8099| 0.0189182| 0.9993075|
## |117998 | 3.6684983| 6433.3212| 0.0191424| 0.9993075|
## |474021 | 3.4369101| 334.4246| 0.0238446| 0.9993075|
## |62840 | 3.7017005| 9809.3585| 0.0315729| 0.9993075|
## |18488 | 2.4623158| 968.3002| 0.0340791| 0.9993075|
## |224095 | 6.1130993| 1655.6526| 0.0361628| 0.9993075|
## |390130 | 3.4669219| 968.7123| 0.0400884| 0.9993075|
## |404049 | 4.0349695| 374.7663| 0.0419526| 0.9993075|
## |3232 | 0.7195349| 10138.8524| 0.0449047| 0.9993075|
## |327608 | 3.9607561| 214.9771| 0.0498798| 0.9993075|
## |17537 | 2.3956932| 511.5029| 0.0505625| 0.9993075|
## |levoglucosan | 0.4128067| 2659.6944| 0.0572881| 0.9993075|
## |62409 | 3.1254274| 1058.0707| 0.0584672| 0.9993075|
## [1] "LS smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue| period|
## |:----------------------|---------:|-----------:|---------:|------:|------:|
## |65238 | 0.0000810| 7359.182| 0.1371420| 1| 8|
## |210229 | 1.7530498| 3610.457| 0.5750968| 1| 8|
## |384970 | 3.1003397| 6021.787| 0.5785948| 1| 8|
## |indole-3-acetate | 0.0000810| 3210.116| 0.5926076| 1| 8|
## |217691 | 3.5289837| 97460.699| 0.6001674| 1| 8|
## |342949 | 6.1238296| 6425.839| 0.6144344| 1| 8|
## |glucose | 7.8534368| 3098740.479| 0.6819300| 1| 8|
## |3-hydroxypropionicacid | 4.0104111| 94252.617| 0.6988460| 1| 8|
## |117998 | 0.6369239| 43853.149| 0.7026137| 1| 8|
## |474021 | 7.8672537| 4448.395| 0.7712369| 1| 8|
## |62840 | 6.0284094| 80416.187| 0.8506479| 1| 8|
## |18488 | 1.9932550| 7111.183| 0.8698372| 1| 8|
## |224095 | 3.9290753| 4587.224| 0.8838802| 1| 8|
## |390130 | 6.0479584| 9183.418| 0.9063269| 1| 8|
## |404049 | 3.9509923| 3099.251| 0.9154042| 1| 8|
## |3232 | 7.9273356| 40515.211| 0.9280115| 1| 8|
## |327608 | 3.6064490| 1943.625| 0.9451552| 1| 8|
## |17537 | 2.0928291| 4898.454| 0.9471655| 1| 8|
## |levoglucosan | 1.6394268| 10481.561| 0.9634413| 1| 8|
## |62409 | 6.3123610| 12988.252| 0.9657302| 1| 8|
## [1] "JTK smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue| period|
## |:----------------------|---------:|-----------:|---------:|------:|------:|
## |1-kestose | 10| 5649.78318| 0.0030173| 1| 12|
## |574694 | 5| 337.82026| 0.0056341| 1| 12|
## |33142 | 3| 13675.79870| 0.0101948| 1| 12|
## |inosine5-monophosphate | 11| 900.14693| 0.0178931| 1| 12|
## |monomyristin | 7| 927.37054| 0.0304890| 1| 12|
## |tocopherolalpha- | 5| 185.26198| 0.0404868| 1| 12|
## |351039 | 11| 2755.94868| 0.0404868| 1| 12|
## |210297 | 4| 11195.62167| 0.0404868| 1| 12|
## |16747 | 5| 4593.01210| 0.0404868| 1| 12|
## |17822 | 3| 6392.95241| 0.0532958| 1| 12|
## |glucose-1-phosphate | 7| 1660.64028| 0.0577981| 1| 12|
## |380205 | 9| 788.77761| 0.0593467| 1| 12|
## |377499 | 3| 453.60900| 0.0732869| 1| 12|
## |arachidicacid | 9| 2701.85501| 0.0771909| 1| 12|
## |31764 | 3| 1197.83889| 0.0771909| 1| 12|
## |threitol | 4| 1132.78506| 0.0855476| 1| 12|
## |tagatose | 4| 8296.83742| 0.0855476| 1| 12|
## |380694 | 7| 2359.61533| 0.0855476| 1| 12|
## |396734 | 5| 98.46462| 0.0900142| 1| 12|
## |384970 | 11| 388.90873| 0.0900142| 1| 12|
## [1] "CS smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue|
## |:----------------------|---------:|----------:|---------:|---------:|
## |1-kestose | 8.831025| 6803.6212| 0.0013484| 0.7766921|
## |33142 | 3.123234| 20417.0351| 0.0028448| 0.8193149|
## |574694 | 3.669047| 346.9884| 0.0072081| 0.9978088|
## |146430 | 0.133065| 1471.0273| 0.0129025| 0.9978088|
## |monomyristin | 7.413849| 1556.3060| 0.0144398| 0.9978088|
## |tocopherolalpha- | 3.786312| 197.4639| 0.0220730| 0.9978088|
## |threitol | 3.572839| 1264.9020| 0.0220742| 0.9978088|
## |187855 | 9.835591| 914.0932| 0.0259425| 0.9978088|
## |phenol | 10.473340| 811.8266| 0.0274826| 0.9978088|
## |351382 | 9.476831| 4332.6468| 0.0295429| 0.9978088|
## |351039 | 9.978655| 4733.4206| 0.0296538| 0.9978088|
## |396734 | 3.696544| 155.3105| 0.0301874| 0.9978088|
## |210297 | 3.242179| 11623.6233| 0.0358363| 0.9978088|
## |inosine5-monophosphate | 9.917336| 1294.2955| 0.0365097| 0.9978088|
## |tagatose | 3.479607| 8155.9157| 0.0379155| 0.9978088|
## |tetracosanol | 10.700610| 307.8580| 0.0391997| 0.9978088|
## |223108 | 9.791170| 975.8067| 0.0398224| 0.9978088|
## |384970 | 9.845686| 481.5084| 0.0412102| 0.9978088|
## |glucose-1-phosphate | 6.479270| 1960.7260| 0.0440687| 0.9978088|
## |67160 | 5.092904| 4607.1118| 0.0454684| 0.9978088|
## [1] "LS smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue| period|
## |:----------------------|---------:|---------:|---------:|------:|------:|
## |1-kestose | 7.998764| 32063.840| 0.1254429| 1| 12|
## |33142 | 4.695473| 82057.334| 0.2151807| 1| 12|
## |574694 | 3.332257| 2603.515| 0.4063947| 1| 12|
## |146430 | 10.868676| 7157.505| 0.5760298| 1| 12|
## |monomyristin | 8.094725| 7227.999| 0.6118720| 1| 12|
## |tocopherolalpha- | 3.779356| 1934.941| 0.7475582| 1| 12|
## |threitol | 5.439673| 7503.613| 0.7475742| 1| 12|
## |187855 | 9.382920| 5607.768| 0.7963329| 1| 12|
## |phenol | 10.667561| 8930.881| 0.8129396| 1| 12|
## |351382 | 8.034932| 21785.759| 0.8330141| 1| 12|
## |351039 | 10.315704| 24653.055| 0.8340300| 1| 12|
## |396734 | 3.908351| 1691.005| 0.8388313| 1| 12|
## |210297 | 1.531069| 58188.299| 0.8817857| 1| 12|
## |inosine5-monophosphate | 10.113036| 9061.608| 0.8860656| 1| 12|
## |tagatose | 6.049842| 44635.492| 0.8945035| 1| 12|
## |tetracosanol | 10.128589| 2806.943| 0.9016615| 1| 12|
## |223108 | 9.640960| 7235.783| 0.9049543| 1| 12|
## |384970 | 11.100340| 6021.787| 0.9119002| 1| 12|
## |glucose-1-phosphate | 6.104174| 15098.118| 0.9246455| 1| 12|
## |67160 | 5.419673| 32043.770| 0.9301955| 1| 12|
## [1] "JTK smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue| period|
## |:------------------------------|---------:|----------:|-------:|--------:|------:|
## |phenylalanine | 19| 19396.1158| 0.0e+00| 1.00e-07| 24|
## |indole-3-propionicacid | 19| 18401.5701| 0.0e+00| 2.00e-07| 24|
## |4-hydroxyhippuricacid | 20| 1394.4146| 0.0e+00| 2.00e-07| 24|
## |tagatose | 8| 18570.7454| 0.0e+00| 2.10e-06| 24|
## |isoleucine | 19| 45891.9372| 0.0e+00| 2.70e-06| 24|
## |553481 | 7| 1452.7509| 0.0e+00| 2.70e-06| 24|
## |3-hydroxy-3-methylglutaricacid | 19| 548.0078| 0.0e+00| 2.70e-06| 24|
## |threitol | 8| 2390.7280| 0.0e+00| 3.10e-06| 24|
## |leucine | 18| 81558.7568| 1.0e-07| 4.70e-06| 24|
## |3-hydroxypropionicacid | 5| 26655.0972| 1.0e-07| 5.50e-06| 24|
## |133969 | 19| 4972.3749| 1.0e-07| 6.90e-06| 24|
## |1981 | 6| 3178.7985| 2.0e-07| 9.80e-06| 24|
## |tryptophan | 20| 14549.7827| 4.0e-07| 1.68e-05| 24|
## |217691 | 5| 28682.7259| 4.0e-07| 1.77e-05| 24|
## |17822 | 9| 16358.2083| 5.0e-07| 1.86e-05| 24|
## |aconiticacid | 8| 7417.0198| 1.1e-06| 4.02e-05| 24|
## |31695 | 20| 921.3601| 1.8e-06| 6.00e-05| 24|
## |quinicacid | 6| 4165.2125| 2.0e-06| 6.36e-05| 24|
## |18256 | 8| 2211.8300| 2.5e-06| 7.18e-05| 24|
## |14730 | 8| 2233.9271| 2.5e-06| 7.18e-05| 24|
## [1] "CS smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue|
## |:------------------------------|---------:|----------:|------:|--------:|
## |tagatose | 7.201829| 18083.1050| 0e+00| 0.00e+00|
## |3-hydroxy-3-methylglutaricacid | 18.671580| 548.4649| 0e+00| 1.00e-07|
## |553481 | 7.593147| 1455.7980| 0e+00| 1.00e-07|
## |phenylalanine | 18.510443| 20500.2894| 0e+00| 1.00e-07|
## |1981 | 5.958649| 3675.2063| 0e+00| 4.00e-07|
## |threitol | 6.738376| 2422.3393| 0e+00| 5.00e-07|
## |18256 | 7.385717| 2111.6032| 0e+00| 1.20e-06|
## |14730 | 7.431546| 2133.1768| 0e+00| 1.30e-06|
## |indole-3-propionicacid | 18.852999| 21303.6994| 0e+00| 2.40e-06|
## |aconiticacid | 7.264334| 6879.7732| 0e+00| 2.40e-06|
## |isoleucine | 18.489847| 46511.0267| 0e+00| 2.40e-06|
## |4-hydroxyhippuricacid | 19.846292| 1856.4436| 1e-07| 2.40e-06|
## |133969 | 18.702631| 4588.5502| 1e-07| 2.40e-06|
## |leucine | 18.550577| 88866.5386| 1e-07| 4.30e-06|
## |2031 | 6.037978| 29889.3277| 1e-07| 4.70e-06|
## |tryptophan | 19.233061| 15938.6354| 2e-07| 6.20e-06|
## |31695 | 18.974324| 1057.3473| 4e-07| 1.19e-05|
## |17822 | 7.758196| 15660.5743| 4e-07| 1.23e-05|
## |163829 | 5.959888| 29149.1644| 4e-07| 1.28e-05|
## |quinicacid | 5.789716| 4643.1234| 6e-07| 1.64e-05|
## [1] "LS smallest p-values"
##
##
## | | acrophase| amplitude| pvalue| qvalue| period|
## |:------------------------------|---------:|----------:|---------:|---------:|------:|
## |tagatose | 6.049842| 44635.492| 0.0000086| 0.0043012| 24|
## |3-hydroxy-3-methylglutaricacid | 18.509994| 1549.453| 0.0000214| 0.0043012| 24|
## |553481 | 6.145246| 4147.245| 0.0000224| 0.0043012| 24|
## |phenylalanine | 18.851962| 85482.672| 0.0000380| 0.0054718| 24|
## |1981 | 4.841687| 9396.851| 0.0000637| 0.0073354| 24|
## |threitol | 5.439673| 7503.613| 0.0000775| 0.0074373| 24|
## |18256 | 6.085036| 5895.532| 0.0001237| 0.0098943| 24|
## |14730 | 6.089501| 5910.170| 0.0001374| 0.0098943| 24|
## |indole-3-propionicacid | 18.613962| 78939.621| 0.0001963| 0.0104774| 24|
## |aconiticacid | 6.092528| 16636.970| 0.0002189| 0.0104774| 24|
## |isoleucine | 19.118363| 224366.115| 0.0002191| 0.0104774| 24|
## |4-hydroxyhippuricacid | 21.999919| 4882.263| 0.0002331| 0.0104774| 24|
## |133969 | 18.692546| 9168.532| 0.0002365| 0.0104774| 24|
## |leucine | 19.364185| 433463.742| 0.0003269| 0.0134484| 24|
## |2031 | 4.506223| 62161.539| 0.0003523| 0.0135278| 24|
## |tryptophan | 19.490921| 75462.718| 0.0004209| 0.0151541| 24|
## |31695 | 21.270865| 5095.172| 0.0006167| 0.0206280| 24|
## |17822 | 6.086638| 63641.387| 0.0006478| 0.0206280| 24|
## |163829 | 4.401658| 60653.107| 0.0006804| 0.0206280| 24|
## |quinicacid | 4.413963| 9580.964| 0.0008024| 0.0229948| 24|#Some examples that were found significant.
library(ggplot2)
test %>% filter(trt == "trf") %>% ggplot(aes(y = tagatose, x = time, color = replicate)) + geom_point() + geom_smooth() + ggtitle("trf")## `geom_smooth()` using method = 'loess' and formula = 'y ~ x'
test %>% filter(trt == "trf") %>% ggplot(aes(y = phenylalanine, x = c_time, color = replicate)) + geom_point() + geom_smooth() + ggtitle("trf")## `geom_smooth()` using method = 'loess' and formula = 'y ~ x'
test %>% filter(trt == "iso") %>% ggplot(aes(y = levoglucosan , x = c_time, color = replicate)) + geom_point() + geom_smooth() + ggtitle("iso")## `geom_smooth()` using method = 'loess' and formula = 'y ~ x'
test %>% filter(trt == "iso") %>% ggplot(aes(y = `520873` , x = c_time, color = replicate)) + geom_point() + geom_smooth() + ggtitle("iso")## `geom_smooth()` using method = 'loess' and formula = 'y ~ x'
test %>% filter(trt == "iso") %>% ggplot(aes(y = `342000` , x = c_time, color = replicate)) + geom_point() + geom_smooth() + ggtitle("iso")## `geom_smooth()` using method = 'loess' and formula = 'y ~ x'